Physical mapping of genomes, e.g., using restriction endonucleases to develop restriction maps, can provide accurate information about the nucleic acid sequences of various organisms. Restriction maps of, e.g., deoxyribonucleic acid (DNA), can be generated by optical mapping. Optical mapping can produce ordered restriction maps by using fluorescence microscopy to visualize restriction endonuclease cutting events on individual labeled DNA molecules.
In optical mapping, nucleic acid is isolated from an organism, deposited on a substrate, and digested by a restriction enzyme. Methods for isolating nucleic acid from an organism, e.g., bacteria, generally involve embedding cells in agarose followed by gentle lysis via enzymatic and/or chemical digestion of a cell wall of the organism. Agarose protects the nucleic acid from fluid turbulence and other shearing forces that otherwise degrade nucleic acid following lysis. The specific combination of enzymes, digestive chemicals, and/or other procedural variants (e.g., pretreatment of cells) depend on a cell wall composition of a particular organism (e.g., Gram positive or negative).
Those methods pose two concerns for rapidly identifying an organism in clinical samples or in contaminated sources. A first problem is that tailoring a lysis protocol is not possible without previous knowledge of the identity of the organism(s) in the source material. A second problem is that agarose or other semi-solid material is not compatible with fluid flow devices used for nucleic acid deposition.
There is a need for methods and kits for isolating nucleic acids from an organism.